Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1983 Jun 11;11(11):3593–3612. doi: 10.1093/nar/11.11.3593

Protection of expressed immunoglobulin genes against nuclease cleavage.

W O Weischet, B O Glotov, H G Zachau
PMCID: PMC325989  PMID: 6304636

Abstract

Fragmentation of the actively transcribed kappa immunoglobulin gene in mouse myeloma nuclei with micrococcal nuclease and the restriction nuclease Bsp RI reveals a chromatin structure without the regularity of repeating nucleosomes found in bulk chromatin. Such regularity is restored about 2.2 kb 3' of the coding region. An only moderately increased micrococcal nuclease sensitivity and a 65% average protection of the Bsp RI sites indicates a DNA-protein interaction in the transcribed region which is not very different from that of an inactive gene. As determined by indirect endlabeling the frequency of Bsp RI cleavage both, after very mild and exhaustive digestion, varied moderately from site to site along the gene. In addition, it was not in each case the same at analogous sites on both alleles which are both transcribed. Thus, the experiments demonstrate differences between the chromatin structures of the genes which may be related to regulatory phenomena and thereby corroborate earlier findings made with DNAase I.

Full text

PDF
3593

Images in this article

3597Image
on p.3597
3599Image
on p.3599
3602Image
on p.3602
3606Image
on p.3606

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altenburger W., Neumaier P. S., Steinmetz M., Zachau H. G. DNA sequence of the constant gene region of the mouse immunoglobulin kappa chain. Nucleic Acids Res. 1981 Feb 25;9(4):971–981. doi: 10.1093/nar/9.4.971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Altenburger W., Steinmetz M., Zachau H. G. Functional and non-functional joining in immunoglobulin light chain genes of a mouse myeloma. Nature. 1980 Oct 16;287(5783):603–607. doi: 10.1038/287603a0. [DOI] [PubMed] [Google Scholar]
  3. Bellard M., Dretzen G., Bellard F., Oudet P., Chambon P. Disruption of the typical chromatin structure in a 2500 base-pair region at the 5' end of the actively transcribed ovalbumin gene. EMBO J. 1982;1(2):223–230. doi: 10.1002/j.1460-2075.1982.tb01151.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bryan P. N., Hofstetter H., Birnstiel M. L. Nucleosome arrangement on tRNA genes of Xenopus laevis. Cell. 1981 Dec;27(3 Pt 2):459–466. doi: 10.1016/0092-8674(81)90387-1. [DOI] [PubMed] [Google Scholar]
  5. Cartwright I. L., Elgin S. C. Analysis of chromatin structure and DNA sequence organization: use of the 1,10-phenanthroline-cuprous complex. Nucleic Acids Res. 1982 Oct 11;10(19):5835–5852. doi: 10.1093/nar/10.19.5835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Early P., Hood L. Allelic exclusion and nonproductive immunoglobulin gene rearrangements. Cell. 1981 Apr;24(1):1–3. doi: 10.1016/0092-8674(81)90492-x. [DOI] [PubMed] [Google Scholar]
  7. Hewish D. R., Burgoyne L. A. Chromatin sub-structure. The digestion of chromatin DNA at regularly spaced sites by a nuclear deoxyribonuclease. Biochem Biophys Res Commun. 1973 May 15;52(2):504–510. doi: 10.1016/0006-291x(73)90740-7. [DOI] [PubMed] [Google Scholar]
  8. Hieter P. A., Max E. E., Seidman J. G., Maizel J. V., Jr, Leder P. Cloned human and mouse kappa immunoglobulin constant and J region genes conserve homology in functional segments. Cell. 1980 Nov;22(1 Pt 1):197–207. doi: 10.1016/0092-8674(80)90168-3. [DOI] [PubMed] [Google Scholar]
  9. Höchtl J., Müller C. R., Zachau H. G. Recombined flanks of the variable and joining segments of immunoglobulin genes. Proc Natl Acad Sci U S A. 1982 Mar;79(5):1383–1387. doi: 10.1073/pnas.79.5.1383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Hörz W., Altenburger W. Sequence specific cleavage of DNA by micrococcal nuclease. Nucleic Acids Res. 1981 Jun 25;9(12):2643–2658. doi: 10.1093/nar/9.12.2643. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hörz W., Igo-Kemenes T., Pfeiffer W., Zachau H. G. Specific cleavage of chromatin by restriction nucleases. Nucleic Acids Res. 1976 Nov;3(11):3213–3226. doi: 10.1093/nar/3.11.3213. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Igo-Kemenes T., Hörz W., Zachau H. G. Chromatin. Annu Rev Biochem. 1982;51:89–121. doi: 10.1146/annurev.bi.51.070182.000513. [DOI] [PubMed] [Google Scholar]
  13. Igo-Kemenes T., Omori A., Zachau H. G. Non-random arrangement of nucleosomes in satellite I containing chromatin of rat liver. Nucleic Acids Res. 1980 Nov 25;8(22):5377–5390. doi: 10.1093/nar/8.22.5377. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Jessee B., Gargiulo G., Razvi F., Worcel A. Analogous cleavage of DNA by micrococcal nuclease and a 1-10-phenanthroline-cuprous complex. Nucleic Acids Res. 1982 Oct 11;10(19):5823–5834. doi: 10.1093/nar/10.19.5823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Levy A., Noll M. Chromatin fine structure of active and repressed genes. Nature. 1981 Jan 15;289(5794):198–203. doi: 10.1038/289198a0. [DOI] [PubMed] [Google Scholar]
  16. Mathis D., Oudet P., Chambon P. Structure of transcribing chromatin. Prog Nucleic Acid Res Mol Biol. 1980;24:1–55. doi: 10.1016/s0079-6603(08)60670-4. [DOI] [PubMed] [Google Scholar]
  17. Max E. E., Maizel J. V., Jr, Leder P. The nucleotide sequence of a 5.5-kilobase DNA segment containing the mouse kappa immunoglobulin J and C region genes. J Biol Chem. 1981 May 25;256(10):5116–5120. [PubMed] [Google Scholar]
  18. Max E. E., Seidman J. G., Leder P. Sequences of five potential recombination sites encoded close to an immunoglobulin kappa constant region gene. Proc Natl Acad Sci U S A. 1979 Jul;76(7):3450–3454. doi: 10.1073/pnas.76.7.3450. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. McGhee J. D., Felsenfeld G. Nucleosome structure. Annu Rev Biochem. 1980;49:1115–1156. doi: 10.1146/annurev.bi.49.070180.005343. [DOI] [PubMed] [Google Scholar]
  20. McGhee J. D., Wood W. I., Dolan M., Engel J. D., Felsenfeld G. A 200 base pair region at the 5' end of the chicken adult beta-globin gene is accessible to nuclease digestion. Cell. 1981 Nov;27(1 Pt 2):45–55. doi: 10.1016/0092-8674(81)90359-7. [DOI] [PubMed] [Google Scholar]
  21. Nedospasov S. A., Georgiev G. P. Non-random cleavage of SV40 DNA in the compact minichromosome and free in solution by micrococcal nuclease. Biochem Biophys Res Commun. 1980 Jan 29;92(2):532–539. doi: 10.1016/0006-291x(80)90366-6. [DOI] [PubMed] [Google Scholar]
  22. Parslow T. G., Granner D. K. Chromatin changes accompany immunoglobulin kappa gene activation: a potential control region within the gene. Nature. 1982 Sep 30;299(5882):449–451. doi: 10.1038/299449a0. [DOI] [PubMed] [Google Scholar]
  23. Pech M., Höchtl J., Schnell H., Zachau H. G. Differences between germ-line and rearranged immunoglobulin V kappa coding sequences suggest a localized mutation mechanism. Nature. 1981 Jun 25;291(5817):668–670. doi: 10.1038/291668a0. [DOI] [PubMed] [Google Scholar]
  24. Pfeiffer W., Horz W., Igo-Kemenes T., Zachau H. G. Restriction nucleases as probes of chromatin structure. Nature. 1975 Dec 4;258(5534):450–452. doi: 10.1038/258450a0. [DOI] [PubMed] [Google Scholar]
  25. Pfeiffer W., Zachau H. G. Accessibility of expressed and non-expressed genes to a restriction nuclease. Nucleic Acids Res. 1980 Oct 24;8(20):4621–4638. doi: 10.1093/nar/8.20.4621. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Sakano H., Hüppi K., Heinrich G., Tonegawa S. Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature. 1979 Jul 26;280(5720):288–294. doi: 10.1038/280288a0. [DOI] [PubMed] [Google Scholar]
  27. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  28. Steinmetz M., Altenburger W., Zachau H. G. A rearranged DNA sequence possibly related to the translocation of immunoglobulin gene segments. Nucleic Acids Res. 1980 Apr 25;8(8):1709–1720. doi: 10.1093/nar/8.8.1709. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Steinmetz M., Zachau H. G. Two rearranged immunoglobulin kappa light chain genes in one mouse myeloma. Nucleic Acids Res. 1980 Apr 25;8(8):1693–1707. doi: 10.1093/nar/8.8.1693. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Storb U., Wilson R., Selsing E., Walfield A. Rearranged and germline immunoglobulin kappa genes: different states of DNase I sensitivity of constant kappa genes in immunocompetent and nonimmune cells. Biochemistry. 1981 Feb 17;20(4):990–996. doi: 10.1021/bi00507a053. [DOI] [PubMed] [Google Scholar]
  31. Tatchell K., Van Holde K. E. Compact oligomers and nucleosome phasing. Proc Natl Acad Sci U S A. 1978 Aug;75(8):3583–3587. doi: 10.1073/pnas.75.8.3583. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Weintraub H., Groudine M. Chromosomal subunits in active genes have an altered conformation. Science. 1976 Sep 3;193(4256):848–856. doi: 10.1126/science.948749. [DOI] [PubMed] [Google Scholar]
  33. Weisbrod S. Active chromatin. Nature. 1982 May 27;297(5864):289–295. doi: 10.1038/297289a0. [DOI] [PubMed] [Google Scholar]
  34. Weischet W. O., Glotov B. O., Schnell H., Zachau H. G. Differences in the nuclease sensitivity between the two alleles of the immunoglobulin kappa light chain genes in mouse liver and myeloma nuclei. Nucleic Acids Res. 1982 Jun 25;10(12):3627–3645. doi: 10.1093/nar/10.12.3627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Wood W. I., Felsenfeld G. Chromatin structure of the chicken beta-globin gene region. Sensitivity to DNase I, micrococcal nuclease, and DNase II. J Biol Chem. 1982 Jul 10;257(13):7730–7736. [PubMed] [Google Scholar]
  36. Wu C., Bingham P. M., Livak K. J., Holmgren R., Elgin S. C. The chromatin structure of specific genes: I. Evidence for higher order domains of defined DNA sequence. Cell. 1979 Apr;16(4):797–806. doi: 10.1016/0092-8674(79)90095-3. [DOI] [PubMed] [Google Scholar]
  37. Wu C. The 5' ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature. 1980 Aug 28;286(5776):854–860. doi: 10.1038/286854a0. [DOI] [PubMed] [Google Scholar]
  38. Wu C., Wong Y. C., Elgin S. C. The chromatin structure of specific genes: II. Disruption of chromatin structure during gene activity. Cell. 1979 Apr;16(4):807–814. doi: 10.1016/0092-8674(79)90096-5. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES